Starting phenix.real_space_refine on Fri Mar 6 00:57:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ws4_32743/03_2026/7ws4_32743.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ws4_32743/03_2026/7ws4_32743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ws4_32743/03_2026/7ws4_32743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ws4_32743/03_2026/7ws4_32743.map" model { file = "/net/cci-nas-00/data/ceres_data/7ws4_32743/03_2026/7ws4_32743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ws4_32743/03_2026/7ws4_32743.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 118 5.16 5 C 16958 2.51 5 N 4371 2.21 5 O 5119 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26566 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 8081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8081 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 8092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8092 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 8088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8088 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 956 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.63, per 1000 atoms: 0.21 Number of scatterers: 26566 At special positions: 0 Unit cell: (138.944, 137.28, 211.328, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 118 16.00 O 5119 8.00 N 4371 7.00 C 16958 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 709 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 709 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 709 " " NAG D 1 " - " ASN C 801 " " NAG E 1 " - " ASN C1074 " " NAG F 1 " - " ASN C1098 " " NAG G 1 " - " ASN C1134 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1074 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN B1134 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN A 717 " " NAG Q 1 " - " ASN A 801 " " NAG R 1 " - " ASN A1098 " " NAG S 1 " - " ASN A1134 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 1.1 seconds 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6240 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 51 sheets defined 23.9% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.602A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.240A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.735A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.038A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.138A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.145A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.553A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN A 957 " --> pdb=" O ASN A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.566A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.506A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.076A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.963A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.536A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.536A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.627A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.041A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.187A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.504A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.587A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.012A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.117A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.898A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.616A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.103A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.137A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.566A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.051A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.409A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.933A pdb=" N ASP I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 87 through 91 removed outlier: 4.144A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.276A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.999A pdb=" N PHE A 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.769A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.107A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.799A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.602A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.960A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.623A pdb=" N ILE A 326 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.778A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.427A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.125A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.674A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.778A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.457A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.374A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.451A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.875A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.972A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.526A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.382A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 13.721A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 13.102A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 10.453A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.071A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.526A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.382A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 317 removed outlier: 3.620A pdb=" N TYR B 313 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.584A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.656A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.029A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.636A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.557A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.948A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.776A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.032A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 135 through 141 removed outlier: 8.043A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 12.109A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.705A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.419A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.219A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.424A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.167A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.633A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.633A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF2, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AF3, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.573A pdb=" N LEU H 105 " --> pdb=" O ALA H 84 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA H 84 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.830A pdb=" N THR I 69 " --> pdb=" O GLN I 82 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AF6, first strand: chain 'I' and resid 58 through 60 removed outlier: 3.678A pdb=" N ASP I 59 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY I 50 " --> pdb=" O ASP I 59 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR I 94 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR I 117 " --> pdb=" O TYR I 94 " (cutoff:3.500A) 1083 hydrogen bonds defined for protein. 2937 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.01 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8377 1.34 - 1.46: 6218 1.46 - 1.58: 12435 1.58 - 1.70: 0 1.70 - 1.83: 148 Bond restraints: 27178 Sorted by residual: bond pdb=" N VAL B 534 " pdb=" CA VAL B 534 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.12e-02 7.97e+03 1.02e+01 bond pdb=" N VAL B 595 " pdb=" CA VAL B 595 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.27e+00 bond pdb=" C ALA B 264 " pdb=" N TYR B 265 " ideal model delta sigma weight residual 1.331 1.289 0.042 1.43e-02 4.89e+03 8.68e+00 bond pdb=" N VAL B 320 " pdb=" CA VAL B 320 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.29e-02 6.01e+03 8.23e+00 bond pdb=" N ASN A 487 " pdb=" CA ASN A 487 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.65e+00 ... (remaining 27173 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 35712 1.52 - 3.03: 1059 3.03 - 4.55: 167 4.55 - 6.06: 33 6.06 - 7.58: 3 Bond angle restraints: 36974 Sorted by residual: angle pdb=" CA ASN B 532 " pdb=" C ASN B 532 " pdb=" O ASN B 532 " ideal model delta sigma weight residual 121.55 117.81 3.74 1.06e+00 8.90e-01 1.25e+01 angle pdb=" CA LYS B 537 " pdb=" C LYS B 537 " pdb=" O LYS B 537 " ideal model delta sigma weight residual 121.38 117.67 3.71 1.06e+00 8.90e-01 1.23e+01 angle pdb=" CA CYS B 538 " pdb=" C CYS B 538 " pdb=" O CYS B 538 " ideal model delta sigma weight residual 122.41 118.22 4.19 1.21e+00 6.83e-01 1.20e+01 angle pdb=" C TYR B 265 " pdb=" N TYR B 266 " pdb=" CA TYR B 266 " ideal model delta sigma weight residual 122.94 128.07 -5.13 1.50e+00 4.44e-01 1.17e+01 angle pdb=" N THR C 19 " pdb=" CA THR C 19 " pdb=" C THR C 19 " ideal model delta sigma weight residual 113.89 108.56 5.33 1.58e+00 4.01e-01 1.14e+01 ... (remaining 36969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 15249 17.88 - 35.77: 1161 35.77 - 53.65: 210 53.65 - 71.53: 62 71.53 - 89.42: 33 Dihedral angle restraints: 16715 sinusoidal: 7027 harmonic: 9688 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 0.86 -86.86 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 177.59 -84.59 1 1.00e+01 1.00e-02 8.69e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -25.11 -60.89 1 1.00e+01 1.00e-02 4.93e+01 ... (remaining 16712 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 3988 0.094 - 0.188: 296 0.188 - 0.281: 5 0.281 - 0.375: 0 0.375 - 0.469: 1 Chirality restraints: 4290 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.49e+00 chirality pdb=" CG LEU H 33 " pdb=" CB LEU H 33 " pdb=" CD1 LEU H 33 " pdb=" CD2 LEU H 33 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA ILE B 598 " pdb=" N ILE B 598 " pdb=" C ILE B 598 " pdb=" CB ILE B 598 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 4287 not shown) Planarity restraints: 4754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO C 987 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 709 " 0.019 2.00e-02 2.50e+03 1.81e-02 4.10e+00 pdb=" CG ASN C 709 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN C 709 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN C 709 " -0.021 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO C 986 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " -0.028 5.00e-02 4.00e+02 ... (remaining 4751 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 483 2.67 - 3.23: 24936 3.23 - 3.78: 40318 3.78 - 4.34: 53877 4.34 - 4.90: 89970 Nonbonded interactions: 209584 Sorted by model distance: nonbonded pdb=" OG1 THR A 323 " pdb=" OE1 GLU A 324 " model vdw 2.110 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.216 3.040 nonbonded pdb=" NZ LYS C 378 " pdb=" OH TYR C 380 " model vdw 2.222 3.120 nonbonded pdb=" O THR C 747 " pdb=" OG SER C 750 " model vdw 2.224 3.040 ... (remaining 209579 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 79 or (resid 80 and (name N or name CA or name \ C or name O or name CB )) or resid 81 through 318 or (resid 319 and (name N or n \ ame CA or name C or name O or name CB )) or resid 320 through 1303)) selection = (chain 'B' and (resid 14 through 500 or (resid 501 and (name N or name CA or nam \ e C or name O or name CB )) or resid 502 through 518 or (resid 519 through 520 a \ nd (name N or name CA or name C or name O or name CB )) or resid 521 through 527 \ or (resid 528 through 529 and (name N or name CA or name C or name O or name CB \ )) or resid 530 through 1303)) selection = (chain 'C' and (resid 14 through 79 or (resid 80 and (name N or name CA or name \ C or name O or name CB )) or resid 81 through 318 or (resid 319 and (name N or n \ ame CA or name C or name O or name CB )) or resid 320 through 500 or (resid 501 \ and (name N or name CA or name C or name O or name CB )) or resid 502 through 13 \ 03)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 23.560 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 27259 Z= 0.211 Angle : 0.633 12.710 37172 Z= 0.346 Chirality : 0.047 0.469 4290 Planarity : 0.004 0.053 4730 Dihedral : 13.510 89.415 10349 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 3269 helix: 1.91 (0.21), residues: 658 sheet: 0.43 (0.18), residues: 759 loop : -0.80 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 19 TYR 0.033 0.001 TYR A 453 PHE 0.026 0.001 PHE A 906 TRP 0.023 0.001 TRP I 47 HIS 0.003 0.001 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00389 (27178) covalent geometry : angle 0.61900 (36974) SS BOND : bond 0.00330 ( 42) SS BOND : angle 1.22849 ( 84) hydrogen bonds : bond 0.12069 ( 1067) hydrogen bonds : angle 6.62521 ( 2937) Misc. bond : bond 0.06899 ( 1) link_BETA1-4 : bond 0.00356 ( 14) link_BETA1-4 : angle 0.84190 ( 42) link_NAG-ASN : bond 0.00370 ( 24) link_NAG-ASN : angle 2.84576 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8293 (m-80) cc_final: 0.7884 (m-80) REVERT: A 515 PHE cc_start: 0.7253 (m-80) cc_final: 0.6793 (m-80) REVERT: B 436 TRP cc_start: 0.7364 (p90) cc_final: 0.6827 (p90) REVERT: C 53 ASP cc_start: 0.7938 (t70) cc_final: 0.7561 (t70) REVERT: C 780 GLU cc_start: 0.8246 (tt0) cc_final: 0.8042 (tt0) REVERT: H 87 TYR cc_start: 0.7462 (m-10) cc_final: 0.7169 (m-10) REVERT: I 74 ASN cc_start: 0.8272 (m-40) cc_final: 0.7558 (m-40) REVERT: I 80 TYR cc_start: 0.7961 (m-80) cc_final: 0.7695 (m-80) REVERT: I 119 VAL cc_start: 0.6722 (m) cc_final: 0.5938 (m) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1651 time to fit residues: 44.3898 Evaluate side-chains 120 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.0970 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 417 ASN B 804 GLN B 935 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN C 474 GLN C 804 GLN C 935 GLN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.091641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.058748 restraints weight = 81640.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.060936 restraints weight = 40531.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.062354 restraints weight = 26841.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.063219 restraints weight = 20886.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.063733 restraints weight = 17927.216| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27259 Z= 0.122 Angle : 0.547 11.279 37172 Z= 0.278 Chirality : 0.045 0.451 4290 Planarity : 0.004 0.047 4730 Dihedral : 6.773 59.398 4366 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.28 % Allowed : 5.30 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.15), residues: 3269 helix: 2.15 (0.21), residues: 662 sheet: 0.44 (0.17), residues: 788 loop : -0.78 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 72 TYR 0.020 0.001 TYR A 453 PHE 0.016 0.001 PHE I 29 TRP 0.009 0.001 TRP I 36 HIS 0.005 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00273 (27178) covalent geometry : angle 0.53450 (36974) SS BOND : bond 0.00333 ( 42) SS BOND : angle 1.11164 ( 84) hydrogen bonds : bond 0.04496 ( 1067) hydrogen bonds : angle 5.36769 ( 2937) Misc. bond : bond 0.00065 ( 1) link_BETA1-4 : bond 0.00402 ( 14) link_BETA1-4 : angle 0.87680 ( 42) link_NAG-ASN : bond 0.00295 ( 24) link_NAG-ASN : angle 2.40432 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8274 (m-80) cc_final: 0.8039 (m-80) REVERT: A 455 LEU cc_start: 0.5193 (mm) cc_final: 0.4977 (mm) REVERT: A 571 ASP cc_start: 0.8240 (t0) cc_final: 0.7819 (t0) REVERT: B 342 PHE cc_start: 0.8703 (m-10) cc_final: 0.7954 (m-10) REVERT: B 436 TRP cc_start: 0.7442 (p90) cc_final: 0.7066 (p90) REVERT: B 1005 GLN cc_start: 0.8822 (tp40) cc_final: 0.8390 (tm-30) REVERT: C 53 ASP cc_start: 0.7945 (t70) cc_final: 0.7672 (t70) REVERT: C 740 MET cc_start: 0.9125 (tpt) cc_final: 0.8860 (tpp) REVERT: C 780 GLU cc_start: 0.8222 (tt0) cc_final: 0.8016 (tt0) REVERT: H 95 PRO cc_start: 0.6104 (Cg_exo) cc_final: 0.5781 (Cg_endo) REVERT: I 119 VAL cc_start: 0.5524 (OUTLIER) cc_final: 0.5090 (t) outliers start: 8 outliers final: 3 residues processed: 140 average time/residue: 0.1713 time to fit residues: 39.3022 Evaluate side-chains 118 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 114 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain I residue 119 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 110 optimal weight: 7.9990 chunk 183 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 190 optimal weight: 0.7980 chunk 300 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 283 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 247 optimal weight: 0.0870 chunk 318 optimal weight: 7.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.091739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.058835 restraints weight = 81641.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.061041 restraints weight = 40505.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.062466 restraints weight = 26811.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.063361 restraints weight = 20824.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.063861 restraints weight = 17867.949| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27259 Z= 0.105 Angle : 0.519 11.114 37172 Z= 0.262 Chirality : 0.044 0.429 4290 Planarity : 0.004 0.050 4730 Dihedral : 6.309 59.675 4366 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.52 % Allowed : 7.05 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.15), residues: 3269 helix: 2.26 (0.21), residues: 659 sheet: 0.52 (0.18), residues: 770 loop : -0.76 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 24 TYR 0.019 0.001 TYR A1067 PHE 0.019 0.001 PHE B 168 TRP 0.009 0.001 TRP H 35 HIS 0.005 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00238 (27178) covalent geometry : angle 0.50716 (36974) SS BOND : bond 0.00280 ( 42) SS BOND : angle 1.03954 ( 84) hydrogen bonds : bond 0.04072 ( 1067) hydrogen bonds : angle 5.10915 ( 2937) Misc. bond : bond 0.00021 ( 1) link_BETA1-4 : bond 0.00355 ( 14) link_BETA1-4 : angle 0.90491 ( 42) link_NAG-ASN : bond 0.00283 ( 24) link_NAG-ASN : angle 2.29151 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: A 515 PHE cc_start: 0.7520 (m-10) cc_final: 0.7217 (m-80) REVERT: A 571 ASP cc_start: 0.8236 (t0) cc_final: 0.7811 (t0) REVERT: B 342 PHE cc_start: 0.8665 (m-10) cc_final: 0.7908 (m-10) REVERT: B 436 TRP cc_start: 0.7504 (p90) cc_final: 0.7069 (p90) REVERT: C 53 ASP cc_start: 0.7998 (t70) cc_final: 0.7688 (t70) REVERT: C 780 GLU cc_start: 0.8211 (tt0) cc_final: 0.7992 (tt0) REVERT: H 24 ARG cc_start: 0.8605 (mmm160) cc_final: 0.8387 (mmm160) REVERT: H 95 PRO cc_start: 0.6255 (Cg_exo) cc_final: 0.5938 (Cg_endo) REVERT: H 97 TYR cc_start: 0.7829 (m-80) cc_final: 0.7315 (m-80) REVERT: I 104 ILE cc_start: 0.7649 (pt) cc_final: 0.6816 (mt) outliers start: 15 outliers final: 7 residues processed: 145 average time/residue: 0.1696 time to fit residues: 39.7457 Evaluate side-chains 128 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 62 PHE Chi-restraints excluded: chain I residue 74 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 200 optimal weight: 0.5980 chunk 203 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 330 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 326 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 323 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 926 GLN A 935 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN C 125 ASN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.091755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.059440 restraints weight = 81385.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.061620 restraints weight = 40635.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.063041 restraints weight = 26947.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.063898 restraints weight = 20990.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.064467 restraints weight = 18012.801| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27259 Z= 0.167 Angle : 0.540 10.423 37172 Z= 0.275 Chirality : 0.044 0.421 4290 Planarity : 0.004 0.050 4730 Dihedral : 6.076 59.923 4366 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.79 % Allowed : 8.67 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.14), residues: 3269 helix: 2.07 (0.21), residues: 674 sheet: 0.36 (0.18), residues: 747 loop : -0.77 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 38 TYR 0.025 0.001 TYR B 265 PHE 0.017 0.001 PHE B 168 TRP 0.018 0.001 TRP H 35 HIS 0.005 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00393 (27178) covalent geometry : angle 0.52784 (36974) SS BOND : bond 0.00343 ( 42) SS BOND : angle 1.17492 ( 84) hydrogen bonds : bond 0.04380 ( 1067) hydrogen bonds : angle 5.06475 ( 2937) Misc. bond : bond 0.00004 ( 1) link_BETA1-4 : bond 0.00285 ( 14) link_BETA1-4 : angle 0.97271 ( 42) link_NAG-ASN : bond 0.00351 ( 24) link_NAG-ASN : angle 2.34127 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.134 Fit side-chains revert: symmetry clash REVERT: A 347 PHE cc_start: 0.7038 (OUTLIER) cc_final: 0.6445 (m-10) REVERT: A 571 ASP cc_start: 0.8201 (t0) cc_final: 0.7767 (t0) REVERT: B 168 PHE cc_start: 0.7816 (t80) cc_final: 0.7373 (t80) REVERT: B 436 TRP cc_start: 0.7630 (p90) cc_final: 0.6929 (p90) REVERT: C 53 ASP cc_start: 0.7971 (t70) cc_final: 0.7761 (t70) REVERT: C 979 ASP cc_start: 0.8484 (m-30) cc_final: 0.8240 (t70) REVERT: H 24 ARG cc_start: 0.8723 (mmm160) cc_final: 0.8380 (mmm160) REVERT: H 95 PRO cc_start: 0.6482 (Cg_exo) cc_final: 0.6179 (Cg_endo) REVERT: H 97 TYR cc_start: 0.7909 (m-80) cc_final: 0.7409 (m-80) REVERT: H 106 GLU cc_start: 0.7991 (pm20) cc_final: 0.7753 (pm20) REVERT: I 104 ILE cc_start: 0.7766 (pt) cc_final: 0.6930 (mt) outliers start: 23 outliers final: 15 residues processed: 150 average time/residue: 0.1634 time to fit residues: 40.6010 Evaluate side-chains 138 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 62 PHE Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 229 optimal weight: 0.8980 chunk 158 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 253 optimal weight: 9.9990 chunk 313 optimal weight: 9.9990 chunk 198 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 301 optimal weight: 0.8980 chunk 257 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.097048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.065468 restraints weight = 80641.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.068525 restraints weight = 45413.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.069005 restraints weight = 26358.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.069247 restraints weight = 24367.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.069560 restraints weight = 23407.371| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27259 Z= 0.167 Angle : 0.546 10.503 37172 Z= 0.276 Chirality : 0.044 0.404 4290 Planarity : 0.004 0.052 4730 Dihedral : 5.868 57.792 4366 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.96 % Allowed : 10.29 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.15), residues: 3269 helix: 2.05 (0.21), residues: 675 sheet: 0.28 (0.18), residues: 760 loop : -0.78 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 493 TYR 0.023 0.001 TYR B 265 PHE 0.030 0.001 PHE H 71 TRP 0.015 0.001 TRP H 35 HIS 0.006 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00391 (27178) covalent geometry : angle 0.53401 (36974) SS BOND : bond 0.00308 ( 42) SS BOND : angle 1.18769 ( 84) hydrogen bonds : bond 0.04371 ( 1067) hydrogen bonds : angle 5.02230 ( 2937) Misc. bond : bond 0.00006 ( 1) link_BETA1-4 : bond 0.00305 ( 14) link_BETA1-4 : angle 0.96443 ( 42) link_NAG-ASN : bond 0.00332 ( 24) link_NAG-ASN : angle 2.29062 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 347 PHE cc_start: 0.7161 (OUTLIER) cc_final: 0.6608 (m-10) REVERT: A 571 ASP cc_start: 0.8181 (t0) cc_final: 0.7755 (t0) REVERT: B 168 PHE cc_start: 0.7908 (t80) cc_final: 0.7467 (t80) REVERT: B 436 TRP cc_start: 0.7739 (p90) cc_final: 0.7231 (p90) REVERT: C 979 ASP cc_start: 0.8494 (m-30) cc_final: 0.8245 (t70) REVERT: H 24 ARG cc_start: 0.8755 (mmm160) cc_final: 0.8347 (mmm160) REVERT: H 88 CYS cc_start: 0.5558 (m) cc_final: 0.5005 (m) REVERT: H 95 PRO cc_start: 0.6505 (Cg_exo) cc_final: 0.6194 (Cg_endo) REVERT: H 97 TYR cc_start: 0.8029 (m-80) cc_final: 0.7479 (m-80) REVERT: H 104 LYS cc_start: 0.8111 (tppt) cc_final: 0.7863 (tppt) REVERT: I 87 ARG cc_start: 0.8646 (mpp80) cc_final: 0.8402 (mpp80) REVERT: I 104 ILE cc_start: 0.7820 (pt) cc_final: 0.7047 (mt) outliers start: 28 outliers final: 18 residues processed: 158 average time/residue: 0.1578 time to fit residues: 41.1690 Evaluate side-chains 144 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 62 PHE Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 74 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 129 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 259 optimal weight: 6.9990 chunk 303 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 217 optimal weight: 9.9990 chunk 281 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 311 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 115 GLN A 965 GLN A1083 HIS B 239 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.104531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.075031 restraints weight = 83138.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.076981 restraints weight = 45716.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.077688 restraints weight = 27695.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.078120 restraints weight = 25882.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.078172 restraints weight = 21794.008| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 27259 Z= 0.276 Angle : 0.647 13.493 37172 Z= 0.327 Chirality : 0.047 0.384 4290 Planarity : 0.004 0.051 4730 Dihedral : 5.997 59.570 4366 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.14 % Allowed : 11.29 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.14), residues: 3269 helix: 1.92 (0.21), residues: 664 sheet: 0.06 (0.18), residues: 763 loop : -0.87 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 983 TYR 0.031 0.002 TYR B 265 PHE 0.019 0.002 PHE A 92 TRP 0.017 0.001 TRP I 47 HIS 0.007 0.002 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00649 (27178) covalent geometry : angle 0.63370 (36974) SS BOND : bond 0.00587 ( 42) SS BOND : angle 1.46680 ( 84) hydrogen bonds : bond 0.05178 ( 1067) hydrogen bonds : angle 5.24897 ( 2937) Misc. bond : bond 0.00002 ( 1) link_BETA1-4 : bond 0.00236 ( 14) link_BETA1-4 : angle 1.09626 ( 42) link_NAG-ASN : bond 0.00546 ( 24) link_NAG-ASN : angle 2.52539 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.7215 (OUTLIER) cc_final: 0.6746 (m-10) REVERT: B 436 TRP cc_start: 0.7899 (p90) cc_final: 0.7255 (p90) REVERT: C 979 ASP cc_start: 0.8558 (m-30) cc_final: 0.8351 (t70) REVERT: C 988 GLU cc_start: 0.8376 (pm20) cc_final: 0.8044 (pm20) REVERT: H 24 ARG cc_start: 0.8750 (mmm160) cc_final: 0.8430 (mmm160) REVERT: H 88 CYS cc_start: 0.5659 (m) cc_final: 0.5258 (m) REVERT: H 95 PRO cc_start: 0.6681 (Cg_exo) cc_final: 0.6388 (Cg_endo) REVERT: H 97 TYR cc_start: 0.8052 (m-80) cc_final: 0.7382 (m-80) REVERT: I 87 ARG cc_start: 0.8665 (mpp80) cc_final: 0.8363 (mpp80) REVERT: I 99 ASP cc_start: 0.8998 (t0) cc_final: 0.8758 (t0) REVERT: I 104 ILE cc_start: 0.7973 (pt) cc_final: 0.7153 (mt) outliers start: 33 outliers final: 24 residues processed: 156 average time/residue: 0.1571 time to fit residues: 40.9288 Evaluate side-chains 148 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 74 optimal weight: 2.9990 chunk 296 optimal weight: 0.8980 chunk 148 optimal weight: 8.9990 chunk 201 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 155 optimal weight: 8.9990 chunk 259 optimal weight: 3.9990 chunk 41 optimal weight: 0.0670 chunk 102 optimal weight: 0.7980 chunk 240 optimal weight: 6.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN B 121 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.094394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.063325 restraints weight = 81828.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.065606 restraints weight = 41199.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.067097 restraints weight = 27395.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.068001 restraints weight = 21353.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.068616 restraints weight = 18251.107| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27259 Z= 0.124 Angle : 0.544 13.351 37172 Z= 0.274 Chirality : 0.044 0.388 4290 Planarity : 0.004 0.055 4730 Dihedral : 5.537 56.932 4366 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.86 % Allowed : 11.91 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 3269 helix: 2.18 (0.21), residues: 664 sheet: 0.30 (0.18), residues: 779 loop : -0.79 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 38 TYR 0.022 0.001 TYR A1067 PHE 0.016 0.001 PHE B 168 TRP 0.016 0.001 TRP I 47 HIS 0.007 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00286 (27178) covalent geometry : angle 0.53178 (36974) SS BOND : bond 0.00356 ( 42) SS BOND : angle 1.31283 ( 84) hydrogen bonds : bond 0.04301 ( 1067) hydrogen bonds : angle 4.96630 ( 2937) Misc. bond : bond 0.00021 ( 1) link_BETA1-4 : bond 0.00351 ( 14) link_BETA1-4 : angle 0.93270 ( 42) link_NAG-ASN : bond 0.00298 ( 24) link_NAG-ASN : angle 2.23553 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: A 347 PHE cc_start: 0.7183 (OUTLIER) cc_final: 0.6792 (m-10) REVERT: A 571 ASP cc_start: 0.8096 (t0) cc_final: 0.7637 (t0) REVERT: B 436 TRP cc_start: 0.7679 (p90) cc_final: 0.7344 (p90) REVERT: B 902 MET cc_start: 0.9098 (tpt) cc_final: 0.8814 (tpt) REVERT: C 988 GLU cc_start: 0.8175 (pm20) cc_final: 0.7916 (pm20) REVERT: H 24 ARG cc_start: 0.8764 (mmm160) cc_final: 0.8404 (mmm160) REVERT: H 95 PRO cc_start: 0.6598 (Cg_exo) cc_final: 0.6297 (Cg_endo) REVERT: H 97 TYR cc_start: 0.7922 (m-80) cc_final: 0.7342 (m-80) REVERT: H 104 LYS cc_start: 0.7553 (tppt) cc_final: 0.7349 (tppt) REVERT: I 87 ARG cc_start: 0.8728 (mpp80) cc_final: 0.8441 (mpp80) REVERT: I 99 ASP cc_start: 0.8932 (t0) cc_final: 0.8601 (t0) REVERT: I 104 ILE cc_start: 0.7809 (pt) cc_final: 0.7032 (mt) outliers start: 25 outliers final: 11 residues processed: 159 average time/residue: 0.1528 time to fit residues: 40.6556 Evaluate side-chains 139 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 74 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 185 optimal weight: 7.9990 chunk 324 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 218 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS A 935 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.092742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.061986 restraints weight = 83284.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.064274 restraints weight = 41556.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.065768 restraints weight = 27305.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.066752 restraints weight = 21169.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.067275 restraints weight = 18026.753| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 27259 Z= 0.203 Angle : 0.601 13.523 37172 Z= 0.302 Chirality : 0.045 0.379 4290 Planarity : 0.004 0.054 4730 Dihedral : 5.473 53.074 4366 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.89 % Allowed : 12.32 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 3269 helix: 2.08 (0.21), residues: 664 sheet: 0.26 (0.18), residues: 781 loop : -0.81 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 983 TYR 0.026 0.001 TYR B 265 PHE 0.030 0.001 PHE I 29 TRP 0.017 0.001 TRP I 47 HIS 0.007 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00478 (27178) covalent geometry : angle 0.58657 (36974) SS BOND : bond 0.00319 ( 42) SS BOND : angle 1.71844 ( 84) hydrogen bonds : bond 0.04652 ( 1067) hydrogen bonds : angle 5.03961 ( 2937) Misc. bond : bond 0.00004 ( 1) link_BETA1-4 : bond 0.00284 ( 14) link_BETA1-4 : angle 1.00546 ( 42) link_NAG-ASN : bond 0.00400 ( 24) link_NAG-ASN : angle 2.34071 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.7234 (OUTLIER) cc_final: 0.6810 (m-10) REVERT: B 436 TRP cc_start: 0.7750 (p90) cc_final: 0.7479 (p90) REVERT: C 478 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7445 (pptt) REVERT: C 988 GLU cc_start: 0.8218 (pm20) cc_final: 0.7960 (pm20) REVERT: H 24 ARG cc_start: 0.8828 (mmm160) cc_final: 0.8472 (mmm160) REVERT: H 95 PRO cc_start: 0.6701 (Cg_exo) cc_final: 0.6405 (Cg_endo) REVERT: H 97 TYR cc_start: 0.8017 (m-80) cc_final: 0.7390 (m-80) REVERT: H 104 LYS cc_start: 0.7835 (tppt) cc_final: 0.7629 (tppt) REVERT: I 87 ARG cc_start: 0.8697 (mpp80) cc_final: 0.8415 (mpp80) REVERT: I 99 ASP cc_start: 0.8981 (t0) cc_final: 0.8666 (t0) REVERT: I 104 ILE cc_start: 0.7868 (pt) cc_final: 0.7108 (mt) outliers start: 26 outliers final: 18 residues processed: 152 average time/residue: 0.1641 time to fit residues: 41.1940 Evaluate side-chains 145 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 74 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 171 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 295 optimal weight: 0.9990 chunk 226 optimal weight: 20.0000 chunk 178 optimal weight: 2.9990 chunk 142 optimal weight: 20.0000 chunk 235 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 279 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.093567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.063938 restraints weight = 83174.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.066147 restraints weight = 45318.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.066407 restraints weight = 28173.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.067021 restraints weight = 25101.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.067101 restraints weight = 22338.714| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 27259 Z= 0.144 Angle : 0.565 12.985 37172 Z= 0.284 Chirality : 0.044 0.375 4290 Planarity : 0.004 0.055 4730 Dihedral : 5.226 53.038 4366 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.83 % Allowed : 12.84 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 3269 helix: 2.17 (0.21), residues: 663 sheet: 0.32 (0.18), residues: 772 loop : -0.78 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 493 TYR 0.021 0.001 TYR A1067 PHE 0.030 0.001 PHE I 29 TRP 0.020 0.001 TRP H 35 HIS 0.007 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00338 (27178) covalent geometry : angle 0.55200 (36974) SS BOND : bond 0.00295 ( 42) SS BOND : angle 1.56531 ( 84) hydrogen bonds : bond 0.04343 ( 1067) hydrogen bonds : angle 4.94040 ( 2937) Misc. bond : bond 0.00008 ( 1) link_BETA1-4 : bond 0.00323 ( 14) link_BETA1-4 : angle 0.94273 ( 42) link_NAG-ASN : bond 0.00309 ( 24) link_NAG-ASN : angle 2.22408 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.7199 (OUTLIER) cc_final: 0.6839 (m-10) REVERT: B 436 TRP cc_start: 0.7668 (p90) cc_final: 0.7353 (p90) REVERT: C 478 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7243 (pptt) REVERT: C 988 GLU cc_start: 0.8376 (pm20) cc_final: 0.7983 (pm20) REVERT: H 24 ARG cc_start: 0.8811 (mmm160) cc_final: 0.8443 (mmm160) REVERT: H 95 PRO cc_start: 0.6548 (Cg_exo) cc_final: 0.6245 (Cg_endo) REVERT: H 97 TYR cc_start: 0.7997 (m-80) cc_final: 0.7367 (m-80) REVERT: I 74 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.8129 (t0) REVERT: I 87 ARG cc_start: 0.8713 (mpp80) cc_final: 0.8421 (mpp80) REVERT: I 99 ASP cc_start: 0.8957 (t0) cc_final: 0.8630 (t0) REVERT: I 104 ILE cc_start: 0.7822 (pt) cc_final: 0.7025 (mt) outliers start: 24 outliers final: 17 residues processed: 150 average time/residue: 0.1612 time to fit residues: 39.7671 Evaluate side-chains 143 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 74 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 266 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 chunk 238 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 282 optimal weight: 1.9990 chunk 243 optimal weight: 6.9990 chunk 72 optimal weight: 0.1980 chunk 325 optimal weight: 7.9990 chunk 202 optimal weight: 0.3980 chunk 142 optimal weight: 20.0000 chunk 279 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 955 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.093942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.063414 restraints weight = 82888.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.065771 restraints weight = 40868.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.067315 restraints weight = 26727.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.068286 restraints weight = 20522.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.068926 restraints weight = 17417.094| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 27259 Z= 0.126 Angle : 0.563 15.039 37172 Z= 0.282 Chirality : 0.044 0.372 4290 Planarity : 0.004 0.055 4730 Dihedral : 5.028 53.270 4366 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.76 % Allowed : 13.21 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.15), residues: 3269 helix: 2.25 (0.21), residues: 657 sheet: 0.37 (0.18), residues: 773 loop : -0.75 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 493 TYR 0.021 0.001 TYR A1067 PHE 0.029 0.001 PHE I 29 TRP 0.034 0.001 TRP H 35 HIS 0.008 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00293 (27178) covalent geometry : angle 0.55092 (36974) SS BOND : bond 0.00270 ( 42) SS BOND : angle 1.50763 ( 84) hydrogen bonds : bond 0.04171 ( 1067) hydrogen bonds : angle 4.89671 ( 2937) Misc. bond : bond 0.00007 ( 1) link_BETA1-4 : bond 0.00327 ( 14) link_BETA1-4 : angle 0.92421 ( 42) link_NAG-ASN : bond 0.00292 ( 24) link_NAG-ASN : angle 2.17024 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.6884 (m-10) REVERT: A 571 ASP cc_start: 0.8103 (t0) cc_final: 0.7644 (t0) REVERT: C 478 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7518 (pptt) REVERT: C 988 GLU cc_start: 0.8144 (pm20) cc_final: 0.7880 (pm20) REVERT: H 24 ARG cc_start: 0.8817 (mmm160) cc_final: 0.8429 (mmm160) REVERT: H 55 GLN cc_start: 0.8165 (tp40) cc_final: 0.7919 (tp-100) REVERT: H 89 GLN cc_start: 0.7260 (tm-30) cc_final: 0.6844 (tm-30) REVERT: H 95 PRO cc_start: 0.6600 (Cg_exo) cc_final: 0.6274 (Cg_endo) REVERT: H 97 TYR cc_start: 0.7990 (m-80) cc_final: 0.7333 (m-80) REVERT: I 74 ASN cc_start: 0.8602 (OUTLIER) cc_final: 0.8214 (t0) REVERT: I 87 ARG cc_start: 0.8652 (mpp80) cc_final: 0.8384 (mpp80) REVERT: I 99 ASP cc_start: 0.8937 (t0) cc_final: 0.8661 (t0) REVERT: I 104 ILE cc_start: 0.7783 (pt) cc_final: 0.7056 (mt) outliers start: 22 outliers final: 17 residues processed: 145 average time/residue: 0.1670 time to fit residues: 40.6625 Evaluate side-chains 144 residues out of total 2916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 74 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 316 optimal weight: 20.0000 chunk 58 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 282 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 269 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 158 optimal weight: 0.7980 chunk 317 optimal weight: 10.0000 chunk 324 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.093287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.063054 restraints weight = 82389.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.066473 restraints weight = 42298.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.066788 restraints weight = 23701.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.067449 restraints weight = 20425.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.067483 restraints weight = 19624.111| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27259 Z= 0.170 Angle : 0.586 13.742 37172 Z= 0.293 Chirality : 0.044 0.361 4290 Planarity : 0.004 0.054 4730 Dihedral : 4.973 53.003 4366 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.79 % Allowed : 13.25 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 3269 helix: 2.17 (0.21), residues: 657 sheet: 0.32 (0.18), residues: 771 loop : -0.77 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 493 TYR 0.023 0.001 TYR B 265 PHE 0.029 0.001 PHE I 29 TRP 0.060 0.002 TRP H 35 HIS 0.009 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00399 (27178) covalent geometry : angle 0.57363 (36974) SS BOND : bond 0.00308 ( 42) SS BOND : angle 1.53662 ( 84) hydrogen bonds : bond 0.04400 ( 1067) hydrogen bonds : angle 4.94550 ( 2937) Misc. bond : bond 0.00002 ( 1) link_BETA1-4 : bond 0.00306 ( 14) link_BETA1-4 : angle 0.96550 ( 42) link_NAG-ASN : bond 0.00347 ( 24) link_NAG-ASN : angle 2.23913 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4684.90 seconds wall clock time: 81 minutes 36.47 seconds (4896.47 seconds total)